Codonopsis pilosula (CP) is a traditional Chinese medicine (TCM) in China, and polysaccharide, as one of its important components, needs to be comprehensively analyzed by combining multiple physicochemical and other characterization means due to its complex intrinsic structure. In this study, the quality of Codonopsis pilosula polysaccharide (CPP) was evaluated by HPGPC profiling and chemometrics. It showed that CPP could be clustered into three groups according to different origins. The polysaccharides were further purified and two different molecular weight polysaccharides (CP-1 and CP-2) were obtained, which contained 80.32 % and 79.05 % of total sugars and 0.73 % and 0.70 % of proteins, respectively, and were acidic and pure, with the average molecular weights of 2568.51 kDa and 3.20 kDa, respectively. The composition of monosaccharides showed that both polysaccharides were composed of glucose, mannose and xylose, but their composition ratios were different, the Glu: Xyl: Man molar ratio of CP-1 was 2.12:1:10.79, and that of CP-2 was 1.25:1:1.41. The infrared spectroscopy analysis showed that there were obvious beta-glycosidic bond and alpha-glycosidic bond and alpha-glycosidic acid in CP-2, and the Congo red test showed that CP-1 had a triple-helical structure, and the SEM results showed that CP-1 had a lamellar structure, while the other had a massive structure. The viscosity of CP-1 was always greater, and the thermodynamic properties of CP-2 was different. Finally, in vitro digestion experiments showed that CP-1 was more resistant to digestion than CP-2. This study provides a reference for the further development and utilization of CPP.